AVR32 Studio 2.0.1 projects have a slightly different build system compared to what was delivered with the 2.0.0 release. Unconverted projects will build and work as usual but build options cannot be changed unless the projects are converted to the 2.0.1 toolchain.
Conversion will not be performed automatically so in order to convert do the following:
If you're upgrading from AVR32 Studio 1.0 you should follow these instructions instead.